Bridging the False Discovery Gap

Controlling the false discovery rate (FDR) among discoveriesfroma tandem mass spectrometry proteomics experiment using target decoycompetition (TDC) controls only the proportion of false discoveriesin an average sense. Thus, for any particular analysis, even witha valid FDR control procedure, the proportion of false discoveries(the FDP) may be higher than the specified FDR threshold. We demonstratethis phenomenon using real data and describe two recently developedmethods that help bridge the gap between controlling the expectedor average rate of false discoveries and the empirical rate (FDP).The FDP Stepdown method controls the FDP at any desired confidencelevel, and the TDC Uniform Band provides a confidence, or upper predictionbound, on the FDP in TDC's list of discoveries.

Automated summary

Controlling the false discovery rate (FDR) in proteomics experiments using target decoy competition (TDC) only controls the average proportion of false discoveries. However, the actual proportion of false discoveries (FDP) may exceed the specified FDR threshold. We demonstrate this using real data and present two methods, FDP Stepdown and TDC Uniform Band, which help bridge the gap between controlling the expected FDR and the empirical FDP.